-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_10/scaffold_10_11442206-11657910

-reading genomic sequence.

** Processing features (+)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: +)
-loading gene prediction evidence. (strand: +)Valid prediction for snap_scaffold_10-snap.2249-T1
Valid prediction for GlimmerHMM_glimmerT_25457-T1
Valid prediction for Augustus_model.g16937.t1
Valid prediction for snap_scaffold_10-snap.2268-T1
Valid prediction for pasa_asmbl_3471.p1
Valid prediction for HiQ_model.g16928.t1
Valid prediction for GlimmerHMM_glimmerT_25468-T1
Valid prediction for GlimmerHMM_glimmerT_25454-T1
Couldn't classify 57714, 57752
Sorry, prediction pasa_asmbl_3469.p1 fails validation.
(TGG)	 AC	57714-57752	GT	AGG
(GGG)	 AG	58211-58358	GT	CTG
(CTC)	 AG	58748-58900	GT	AGG
(ACA)	 AG	59461-59635	GT	GGG
(AGG)	 AG	60885-61025	GT	CGG
(GTC)	 AG	61500-61623	GT	AGG
(GTG)	 AG	62641-62709	GT	AGG
(GTG)	 AG	62841-63015	GT	AGG
(GTC)	 AG	63310-63408	GT	TCG
(CTC)	 AG	63531-63622	GT	AGG
(GGA)	 AG	64160-64207	AA	GAA
-recovered pasa_asmbl_3469.p1, terminal, 64160, 64207
-recovered pasa_asmbl_3469.p1, internal, 58211, 58358
-recovered pasa_asmbl_3469.p1, internal, 58748, 58900
-recovered pasa_asmbl_3469.p1, internal, 59461, 59635
-recovered pasa_asmbl_3469.p1, internal, 60885, 61025
-recovered pasa_asmbl_3469.p1, internal, 61500, 61623
-recovered pasa_asmbl_3469.p1, internal, 62641, 62709
-recovered pasa_asmbl_3469.p1, internal, 62841, 63015
-recovered pasa_asmbl_3469.p1, internal, 63310, 63408
-recovered pasa_asmbl_3469.p1, internal, 63531, 63622
Valid prediction for pasa_asmbl_3474.p1
Valid prediction for pasa_asmbl_3462.p1
Valid prediction for snap_scaffold_10-snap.2264-T1
Valid prediction for Augustus_model.g16939.t1
Valid prediction for snap_scaffold_10-snap.2251-T1
Valid prediction for snap_scaffold_10-snap.2254-T1
Valid prediction for GlimmerHMM_glimmerT_25465-T1
Valid prediction for snap_scaffold_10-snap.2267-T1
Valid prediction for HiQ_model.g16925.t1
Valid prediction for snap_scaffold_10-snap.2255-T1
Valid prediction for GlimmerHMM_glimmerT_25459-T1
Valid prediction for CodingQuarry_transcript_5572-T1
Valid prediction for CodingQuarry_transcript_5571-T1
Valid prediction for GlimmerHMM_glimmerT_25466-T1
Valid prediction for snap_scaffold_10-snap.2266-T1
Valid prediction for snap_scaffold_10-snap.2257-T1
Couldn't classify 196260, 196413
Sorry, prediction pasa_asmbl_3491.p1 fails validation.
(CTA)	 AG	196260-196413	GT	GGG
(AAA)	 AG	196639-196690	GT	ATG
(GCC)	 AG	197300-197376	GT	TGG
(ACT)	 AG	197735-197751	TC	AAT
-recovered pasa_asmbl_3491.p1, terminal, 197735, 197751
-recovered pasa_asmbl_3491.p1, internal, 196260, 196413
-recovered pasa_asmbl_3491.p1, internal, 196639, 196690
-recovered pasa_asmbl_3491.p1, internal, 197300, 197376
Valid prediction for GlimmerHMM_glimmerT_25463-T1
Couldn't classify 196689, 196690
Sorry, prediction CodingQuarry_transcript_5574-T1 fails validation.
(ATG)	 CA	196689-196690	GT	ATG
(GCC)	 AG	197300-197376	GT	TGG
(ACT)	 AG	197735-197751	TC	AAT
-recovered CodingQuarry_transcript_5574-T1, terminal, 197735, 197751
-recovered CodingQuarry_transcript_5574-T1, internal, 197300, 197376
Valid prediction for Augustus_model.g16940.t1
Valid prediction for pasa_asmbl_3489.p1
Valid prediction for snap_scaffold_10-snap.2248-T1
Valid prediction for pasa_asmbl_3459.p2
Valid prediction for HiQ_model.g16933.t1
Valid prediction for Augustus_model.g16929.t1
Valid prediction for snap_scaffold_10-snap.2261-T1
Valid prediction for Augustus_model.g16930.t1
Valid prediction for snap_scaffold_10-snap.2271-T1
Valid prediction for snap_scaffold_10-snap.2252-T1
Valid prediction for GlimmerHMM_glimmerT_25461-T1
Valid prediction for Augustus_model.g16934.t1
Valid prediction for snap_scaffold_10-snap.2270-T1
Valid prediction for GlimmerHMM_glimmerT_25462-T1
Valid prediction for CodingQuarry_transcript_5570-T1
Valid prediction for snap_scaffold_10-snap.2242-T1
Valid prediction for snap_scaffold_10-snap.2259-T1
Valid prediction for HiQ_model.g16935.t1
Valid prediction for snap_scaffold_10-snap.2247-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_25451-T1
Valid prediction for Augustus_model.g16932.t1
Valid prediction for GlimmerHMM_glimmerT_25452-T1
Couldn't classify 52023, 52128
Couldn't classify 56238, 56334
Sorry, prediction pasa_asmbl_3464.p1 fails validation.
(AAC)	 AT	52023-52128	GT	CAG
(TCA)	 AG	52516-52662	GT	AGG
(GTG)	 AG	52867-53018	GT	AGG
(GTG)	 AG	53302-53437	GT	AGG
(GTA)	 AG	53773-53864	GT	AGG
(GTT)	 AG	54067-54199	GT	AGG
(AGA)	 AG	55430-55508	GT	AGG
(GAA)	 AG	56238-56334	GT	AGG
-recovered pasa_asmbl_3464.p1, internal, 52516, 52662
-recovered pasa_asmbl_3464.p1, internal, 52867, 53018
-recovered pasa_asmbl_3464.p1, internal, 53302, 53437
-recovered pasa_asmbl_3464.p1, internal, 53773, 53864
-recovered pasa_asmbl_3464.p1, internal, 54067, 54199
-recovered pasa_asmbl_3464.p1, internal, 55430, 55508
-recovered pasa_asmbl_3464.p1, internal, 56238, 56334
Valid prediction for GlimmerHMM_glimmerT_25456-T1
Valid prediction for snap_scaffold_10-snap.2245-T1
Valid prediction for pasa_asmbl_3486.p1
Couldn't classify 147449, 147519
Sorry, prediction pasa_asmbl_3477.p1 fails validation.
(GCG)	 AG	147449-147519	GT	GAG
(GCT)	 AG	147714-147783	GT	TTG
(GAC)	 AG	147938-148044	GT	AAG
(GGA)	 AG	148129-148159	GT	ATG
(GTG)	 AG	148572-148682	GT	CAG
(GAG)	 AG	149328-149452	GT	AGG
(CTT)	 AG	150053-150123	GT	TGG
(TTG)	 AG	150799-150988	GT	AGG
(CTG)	 AG	151315-151578	GT	AGG
(CGT)	 AG	152076-152402	GT	AGG
(TGA)	 AG	152625-152894	GT	AGG
(TGA)	 AG	153812-154069	GT	AGG
(ATT)	 AG	154608-155015	GT	AGG
(AGC)	 AG	155298-155639	GT	AGG
(CAT)	 AG	156126-156479	GT	ATG
(GAT)	 AG	157049-157087	GT	GAG
(GAG)	 AG	157589-157718	GT	ATG
(GAC)	 AG	157799-157956	GT	AAG
(GGA)	 AG	158146-158905	GT	AGG
(GTG)	 AG	159023-159334	GT	AGG
(GTC)	 AG	159453-159561	GT	AGG
(AAG)	 AG	159695-159720	GT	CTG
(ATT)	 AG	159911-160024	GT	AGG
(GAG)	 AG	160254-160346	GT	AGG
(GAG)	 AG	160456-160726	GT	AGG
(ATG)	 AG	160811-160904	GT	AGG
(GTC)	 AG	161324-161392	GT	AGG
(ATG)	 AG	161686-161794	GT	AGG
(TGT)	 AG	162074-162176	GT	TGG
(CAG)	 AG	162500-162522	TA	GAT
-recovered pasa_asmbl_3477.p1, initial, 160811, 160904
add_exon() Sorry, pasa_asmbl_3477.p1 161686-161794-initial-1 is invalid.
-recovered pasa_asmbl_3477.p1, initial, 161686, 161794
-recovered pasa_asmbl_3477.p1, terminal, 162500, 162522
-recovered pasa_asmbl_3477.p1, internal, 147449, 147519
-recovered pasa_asmbl_3477.p1, internal, 147714, 147783
-recovered pasa_asmbl_3477.p1, internal, 147938, 148044
-recovered pasa_asmbl_3477.p1, internal, 148129, 148159
-recovered pasa_asmbl_3477.p1, internal, 148572, 148682
-recovered pasa_asmbl_3477.p1, internal, 149328, 149452
-recovered pasa_asmbl_3477.p1, internal, 150053, 150123
-recovered pasa_asmbl_3477.p1, internal, 150799, 150988
-recovered pasa_asmbl_3477.p1, internal, 151315, 151578
-recovered pasa_asmbl_3477.p1, internal, 152076, 152402
-recovered pasa_asmbl_3477.p1, internal, 152625, 152894
-recovered pasa_asmbl_3477.p1, internal, 153812, 154069
-recovered pasa_asmbl_3477.p1, internal, 154608, 155015
-recovered pasa_asmbl_3477.p1, internal, 155298, 155639
-recovered pasa_asmbl_3477.p1, internal, 156126, 156479
-recovered pasa_asmbl_3477.p1, internal, 157049, 157087
-recovered pasa_asmbl_3477.p1, internal, 157589, 157718
-recovered pasa_asmbl_3477.p1, internal, 157799, 157956
-recovered pasa_asmbl_3477.p1, internal, 158146, 158905
-recovered pasa_asmbl_3477.p1, internal, 159023, 159334
-recovered pasa_asmbl_3477.p1, internal, 159453, 159561
-recovered pasa_asmbl_3477.p1, internal, 159695, 159720
-recovered pasa_asmbl_3477.p1, internal, 159911, 160024
-recovered pasa_asmbl_3477.p1, internal, 160254, 160346
-recovered pasa_asmbl_3477.p1, internal, 160456, 160726
-recovered pasa_asmbl_3477.p1, internal, 160811, 160904
-recovered pasa_asmbl_3477.p1, internal, 161324, 161392
-recovered pasa_asmbl_3477.p1, internal, 161686, 161794
-recovered pasa_asmbl_3477.p1, internal, 162074, 162176

-loading the search evidence (protein and EST search results, strand: +)
-scoring exons (strand: +)

** Processing features (-)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: -)
-loading gene prediction evidence. (strand: -)Valid prediction for GlimmerHMM_glimmerT_25453-T1
Valid prediction for GlimmerHMM_glimmerT_25471-T1
Valid prediction for Augustus_model.g16931.t1
Valid prediction for pasa_asmbl_4783.p1
Valid prediction for GlimmerHMM_glimmerT_25467-T1
Valid prediction for snap_scaffold_10-snap.2250-T1
Valid prediction for GlimmerHMM_glimmerT_25470-T1
Valid prediction for pasa_asmbl_4778.p1
Valid prediction for Augustus_model.g16926.t1
Valid prediction for snap_scaffold_10-snap.2265-T1
Valid prediction for snap_scaffold_10-snap.2256-T1
Valid prediction for CodingQuarry_transcript_5573-T1
Valid prediction for snap_scaffold_10-snap.2269-T1
Valid prediction for GlimmerHMM_glimmerT_25464-T1
Valid prediction for GlimmerHMM_glimmerT_25469-T1
Valid prediction for snap_scaffold_10-snap.2258-T1
Valid prediction for snap_scaffold_10-snap.2262-T1
Valid prediction for snap_scaffold_10-snap.2246-T1
Valid prediction for snap_scaffold_10-snap.2243-T1
Valid prediction for Augustus_model.g16936.t1
Valid prediction for GlimmerHMM_glimmerT_25458-T1
Valid prediction for GlimmerHMM_glimmerT_25450-T1
Couldn't classify 201522, 201894
Couldn't classify 202309, 202337
Sorry, prediction pasa_asmbl_5125.p1 fails validation.
(GGG)	 AG	201522-201894	GT	AGG
(CCA)	 AG	202042-202149	GT	AAG
(TTT)	 AG	202309-202337	CC	CTC
-recovered pasa_asmbl_5125.p1, internal, 201522, 201894
-recovered pasa_asmbl_5125.p1, internal, 202042, 202149
Valid prediction for snap_scaffold_10-snap.2253-T1
Valid prediction for HiQ_model.g16938.t1
Valid prediction for GlimmerHMM_glimmerT_25460-T1
Valid prediction for GlimmerHMM_glimmerT_25455-T1
Valid prediction for snap_scaffold_10-snap.2263-T1
Valid prediction for snap_scaffold_10-snap.2260-T1
Valid prediction for Augustus_model.g16927.t1
Valid prediction for snap_scaffold_10-snap.2244-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 55780, rend_intergenic: 53248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59188, rend_intergenic: 56215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104664, rend_intergenic: 103319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142777, rend_intergenic: 139282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162522, rend_intergenic: 144499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171740, rend_intergenic: 170689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186073, rend_intergenic: 179521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 215705
-exon list size: 338


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
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2.1    
2.4    
2.6    
2.9    
3.2    
3.5    
3.8    
4.1    
4.4    
4.7    
5.0    
5.3    
5.6    
5.9    
6.2    
6.5    
6.8    
7.1    
7.4    
7.6    
7.9    
8.2    
8.5    
8.8    
9.1    
9.4    
9.7    
10.0    
10.3    
10.6    
10.9    
11.2    
11.5    
11.8    
12.1    
12.4    
12.6    
12.9    
13.2    
13.5    
13.8    
14.1    
14.4    
14.7    
15.0    
15.3    
15.6    
15.9    
16.2    
16.5    
16.8    
17.1    
17.4    
17.6    
17.9    
18.2    
18.5    
18.8    
19.1    
19.4    
19.7    
20.0    
20.3    
20.6    
20.9    
21.2    
21.5    
21.8    
22.1    
22.4    
22.6    
22.9    
23.2    
23.5    
23.8    
24.1    
24.4    
24.7    
25.0    
25.3    
25.6    
25.9    
26.2    
26.5    
26.8    
27.1    
27.4    
27.6    
27.9    
28.2    
28.5    
28.8    
29.1    
29.4    
29.7    
30.0    
30.3    
30.6    
30.9    
31.2    
31.5    
31.8    
32.1    
32.4    
32.6    
32.9    
33.2    
33.5    
33.8    
34.1    
34.4    
34.7    
35.0    
35.3    
35.6    
35.9    
36.2    
36.5    
36.8    
37.1    
37.4    
37.6    
37.9    
38.2    
38.5    
38.8    
39.1    
39.4    
39.7    
40.0    
40.3    
40.6    
40.9    
41.2    
41.5    
41.8    
42.1    
42.4    
42.6    
42.9    
43.2    
43.5    
43.8    
44.1    
44.4    
44.7    
45.0    
45.3    
45.6    
45.9    
46.2    
46.5    
46.8    
47.1    
47.4    
47.6    
47.9    
48.2    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.8    
52.1    
52.4    
52.6    
52.9    
53.2    
53.5    
53.8    
54.1    
54.4    
54.7    
55.0    
55.3    
55.6    
55.9    
56.2    
56.5    
56.8    
57.1    
57.4    
57.6    
57.9    
58.2    
58.5    
58.8    
59.1    
59.4    
59.7    
60.0    
60.3    
60.6    
60.9    
61.2    
61.5    
61.8    
62.1    
62.4    
62.6    
62.9    
63.2    
63.5    
63.8    
64.1    
64.4    
64.7    
65.0    
65.3    
65.6    
65.9    
66.2    
66.5    
66.8    
67.1    
67.4    
67.6    
67.9    
68.2    
68.5    
68.8    
69.1    
69.4    
69.7    
70.0    
70.3    
70.6    
70.9    
71.2    
71.5    
71.8    
72.1    
72.4    
72.6    
72.9    
73.2    
73.5    
73.8    
74.1    
74.4    
74.7    
75.0    
75.3    
75.6    
75.9    
76.2    
76.5    
76.8    
77.1    
77.4    
77.6    
77.9    
78.2    
78.5    
78.8    
79.1    
79.4    
79.7    
80.0    
80.3    
80.6    
80.9    
81.2    
81.5    
81.8    
82.1    
82.4    
82.6    
82.9    
83.2    
83.5    
83.8    
84.1    
84.4    
84.7    
85.0    
85.3    
85.6    
85.9    
86.2    
86.5    
86.8    
87.1    
87.4    
87.6    
87.9    
88.2    
88.5    
88.8    
89.1    
89.4    
89.7    
90.0    
90.3    
90.6    
90.9    
91.2    
91.5    
91.8    
92.1    
92.4    
92.6    
92.9    
93.2    
93.5    
93.8    
94.1    
94.4    
94.7    
95.0    
95.3    
95.6    
95.9    
96.2    
96.5    
96.8    
97.1    
97.4    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 55780, rend_intergenic: 53248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59188, rend_intergenic: 56215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104664, rend_intergenic: 103319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142777, rend_intergenic: 139282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162522, rend_intergenic: 144499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171740, rend_intergenic: 170689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186073, rend_intergenic: 179521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support